Complicating matters further, the Pentagon and Lockheed have been at war with each other for years. Air Force Lieut. General Christopher Bogdan, a senior Pentagon F-35 manager, declared last summer that the relationship was "the worst I've ever seen--and I've been in some bad ones." But the two sides insist the worst is now behind them. Lockheed CEO Marillyn Hewson said last month that the aircraft has topped 5,000 flight hours, stepped up its flight-test schedule and is steadily pushing into new corners of its flight envelope. "Our maturing production line, operational-base stand-up and expanded pilot training are all strong indicators of the F-35 program's positive trajectory," she said. Deliveries of fresh F-35s more than doubled in 2012, to 30 planes.

Pilots love the F-35. There are few gauges, buttons or knobs in the cockpit. "What you have in front of you is a big touchscreen display--it's an interface for the iPad generation," says Marine Colonel Arthur Tomassetti, an F-35 test pilot. "You have an airplane that with very small movements of your left and right hand does what you want it to do. And if you don't want it to do anything, it stays where you left it." That makes it easy to fly. "I'm watching the emerald-colored sea up against the white sand," Tomassetti says of his flights from Florida's Eglin Air Force Base along the shore of the Gulf of Mexico. "I remember lots of flights in other airplanes where I never had time to do anything like that."

But military technology has been moving away from manned fighters for years. Drones, standoff weapons and GPS-guided bombs have cut the utility of, and need for, such short-leg piloted planes. Their limits become even more pronounced amid the Pentagon's pivot to the Pacific, where the tyranny of distance makes the F-35's short combat radius (469 miles for the Marines, 584 for the Air Force, 615 for the Navy) a bigger challenge.

Computers are key to flying the plane. But instead of taking advantage of simplicity, the F-35 is heading in the other direction: its complexity can be gleaned from its 24 million lines of computer code, including 9.5 million on board the plane. That's more than six times as much as the Navy F-18 has. The F-35 computer code, government auditors say, is "as complicated as anything on earth."

Computers also were supposed to replace most prototyping and allow all three kinds of F-35s to roll off the Texas assembly line at the same time, just as Avalons, Camrys and Venzas are rolling out of Toyota's huge Kentucky plant. "Advances in the technology, in our design tools and in our manufacturing processes have significantly changed the manner in which aircraft are designed and built today," Paul Kaminski, the Pentagon's top weapons buyer, said in 1997.

But Lockheed is no Toyota. Aviation Week & Space Technology magazine, the bible of the aerospace industry and a traditional supporter, published an editorial last fall that declared the program "already a failure" on cost and schedule and said "the jury is still out" on its capabilities. It suggested pitting the F-35 against existing fighters--Air Force F-15s and F-16s and Navy F-18s--for future U.S. fighter purchases.